Strain identifier

BacDive ID: 13408

Type strain: Yes

Species: Pseudonocardia kunmingensis

Strain history: CCTCC AA 208078 <-- W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 63158.

NCBI tax ID(s): 630975 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16157

BacDive-ID: 13408

DSM-Number: 45301

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Pseudonocardia kunmingensis DSM 45301 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized roots of Artemisia annua L..

NCBI tax id

  • NCBI tax id: 630975
  • Matching level: species

strain history

@refhistory
16157<- S.-K. Tang, Yunnan Univ., Kunming; YIM 63158 <- G.-Z. Zhao
67770CCTCC AA 208078 <-- W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 63158.

doi: 10.13145/bacdive13408.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia kunmingensis
  • full scientific name: Pseudonocardia kunmingensis Zhao et al. 2011

@ref: 16157

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia kunmingensis

full scientific name: Pseudonocardia kunmingensis Zhao et al. 2011

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
21427Sand yellow (1002)10-14 daysISP 2
21427Light ivory (1015)10-14 daysISP 3
21427Light ivory (1015)10-14 daysISP 4
21427Zinc yellow (1018)10-14 daysISP 5
21427Sand yellow (1002)10-14 daysISP 6
21427Beige (1001)10-14 daysISP 7
21427Grey beige (1019)10-14 daysSuter with tyrosine
21427Zinc yellow (1018)10-14 daysSuter without tyrosine

multimedia

  • @ref: 16157
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45301.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16157GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
21427ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21427ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21427ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21427ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21427ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
21427ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21427Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21427Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
16157positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 98.531

halophily

  • @ref: 21427
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2142717234glucose+
2142722599arabinose+
2142717992sucrose+
2142718222xylose+
2142717268myo-inositol+
2142737684mannose+
2142728757fructose+
2142726546rhamnose+
2142716634raffinose+
2142762968cellulose+
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin-3.4.21.4
68382acid phosphatase+3.1.3.2
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-fucosidase+3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21427---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21427+++/-+/-+++/--+/-++/-+/-+-++-+/-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16157surface-sterilized roots of Artemisia annua L.Artemisia annuaYunnan Province, KunmingChinaCHNAsia
67770Surface-sterilized roots of Artemisia annua L. from KunmingArtemisia annuaYunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
161571Risk group (German classification)
21427L1German classification

Sequence information

16S sequences

  • @ref: 16157
  • description: Pseudonocardia kunmingensis strain YIM 63158 16S ribosomal RNA gene, partial sequence
  • accession: FJ817377
  • length: 1388
  • database: ena
  • NCBI tax ID: 630975

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia kunmingensis strain DSM 45301630975.3wgspatric630975
66792Pseudonocardia kunmingensis DSM 453012816332139draftimg630975
67770Pseudonocardia kunmingensis DSM 45301GCA_006716445contigncbi630975

GC content

  • @ref: 16157
  • GC-content: 73.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes84no
gram-positiveyes85.792no
anaerobicno98.908no
halophileno82.921no
spore-formingyes77.433no
glucose-utilyes84.456no
thermophileno99.145yes
flagellatedno98.265no
aerobicyes93.818no
motileno90.966no
glucose-fermentno88.502yes

External links

@ref: 16157

culture collection no.: DSM 45301, CCTCC AA 208078, YIM 63158, JCM 32122

straininfo link

  • @ref: 82605
  • straininfo: 397791

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20971834Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L.Zhao GZ, Li J, Huang HY, Zhu WY, Park DJ, Kim CJ, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.027607-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Artemisia annua/*microbiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny24198055Pseudonocardia sediminis sp. nov., isolated from marine sediment.Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM, Tian XP, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.057844-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
16157Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45301)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45301
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
21427Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45301.pdfCompendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
82605Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397791.1StrainInfo: A central database for resolving microbial strain identifiers